align.clustalw: Multiple sequence alignment by means of ClustalW
In MEET: MEET: Motif Elements Estimation Toolkit
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
View source: R/align.clustalw.R
Description
DNA sequences are aligned by means of ClustalW (Multiple Sequence Alignment).
Usage
1
align.clustalw(filein , fileout = "Sq.fa", call)
Arguments
filein
A set of nucleotide sequences in FASTA format.
fileout
Output file in FASTA format.
call
string of characters needed to call Clustalw from the working directory
Details
This function needs aaMI-package
Value
Fileout is a file in FASTA format with aligned nucleotide sequences.
Author(s)
Erola Pairo <epairo@ibecbarcelona.eu> and Joan Maynou <joan.maynou@upc.edu>.
References
J. Thompson, D. Higgins, and T. Gibson, Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice, Nucleic Acids Res., vol. 22, 1994.
See Also
align.MEME, align.MUSCLE
Examples
1
2
pathMEET<-system.file("exdata",package="MEET")
#align.clustalw(filein=paste(pathMEET,"AP1.fa",sep="/"), fileout="Sq.fa",call=call.clustalw)
MEET documentation built on May 2, 2019, 5:52 p.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/align.clustalw.R
Description
DNA sequences are aligned by means of ClustalW (Multiple Sequence Alignment).
Usage
1 | align.clustalw(filein , fileout = "Sq.fa", call)
|
Arguments
filein |
A set of nucleotide sequences in FASTA format. |
fileout |
Output file in FASTA format. |
call |
string of characters needed to call Clustalw from the working directory |
Details
This function needs aaMI-package
Value
Fileout is a file in FASTA format with aligned nucleotide sequences.
Author(s)
Erola Pairo <epairo@ibecbarcelona.eu> and Joan Maynou <joan.maynou@upc.edu>.
References
J. Thompson, D. Higgins, and T. Gibson, Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice, Nucleic Acids Res., vol. 22, 1994.
See Also
align.MEME, align.MUSCLE
Examples
1 2 | pathMEET<-system.file("exdata",package="MEET")
#align.clustalw(filein=paste(pathMEET,"AP1.fa",sep="/"), fileout="Sq.fa",call=call.clustalw)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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